The strike, which was in its second day, had left loading and unloading at a standstill. A separate strike by workers demanding better pay halted operations by Kenya Ferry Services.
The main gateway for East Africa's trade, Mombasa handles imports such as fuel for Uganda, Burundi, Rwanda, South Sudan, eastern Democratic Republic of Congo and Somalia.
Simon Sang, secretary general of the dock workers union, told workers the dispute had been resolved after most of their employment letters were signed.
"Go to your departments. All letters have been dispatched to the departments. Pick your letter and go back to work," he said.
"Our most important demand has been granted," he told jubilant workers, who pumped fists in the air in celebration.
An official at the Kenya Ports Authority's (KPA) said the union had agreed to send the workers back to their jobs after receiving their letters.
"They are back to work," the official, who declined to be named, told Reuters.
Dockside work resumed gradually as workers trickled back after collecting their letters of employment, which guaranteed them a pension scheme.
Others chanted slogans outside the port's main offices as they lined up to get their letters.
"It feels a lot better now. At least I am assured of a hefty package when I retire," said Juma Kassim, a crane operator.
"I don't know why the port had to wait until we forced them by striking. I'm sure the port has suffered great losses."
Hundreds of tons of cargo were piled up.
"We arrived here yesterday morning to collect containers destined for Rwanda, but there is nobody to load them on the trucks. We just spent the night out here in the cold," said Colyns Mutua, a long-distance truck driver.
Labour unrest has increased in east Africa's biggest economy this year following steep price increases and ahead of presidential and parliamentary elections next March. Teachers, university lecturers and doctors have also staged strikes to demand better pay and working conditions.
The ferry strike blocked trucks, carrying fuel, food and goods, and office workers from the mainland who were trying to get to work on Mombasa island.
Tourists at the coastal strip popular with Kenyan and foreign holidaymakers, who were hoping to get to the main airport from beach luxury resorts, were left stranded.
The nearest alternative route into the island requires a detour of about 80 km. (Reuters)
